From a pure structural perspective, the designation of the two strands in an anti-parallel DNA duplex is sort of arbitrary. Thus, for a given PDB file, let’s assume that the atomic coordinates of chain A (strand I) come before those of chain B (strand II). We can swap the order of the two chains as they appear in the PDB file, i.e., list first the atomic coordinates of chain B and then those of chain A.
Structurally, the two settings corresponding to exactly the same DNA molecule. As far as 3DNA goes, however, the different orderings do make a different in calculated parameters. Using the Dickerson B-DNA dodecamer CGCGAATTCGCG solved at high resolution (PDB entry 355d) as an example, running 3DNA find_pair and analyze on ‘355d.pdb’ gives the results (abbreviated) below:
find_pair 355d.pdb 355d.bps
# contents of file '355d.bps':
------------------------------------------------------------------
355d.pdb
355d.out
2 # duplex
12 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
1 24 0 # 1 | ....>A:...1_:[.DC]C-----G[.DG]:..24_:B<....
2 23 0 # 2 | ....>A:...2_:[.DG]G-----C[.DC]:..23_:B<....
3 22 0 # 3 | ....>A:...3_:[.DC]C-----G[.DG]:..22_:B<....
4 21 0 # 4 | ....>A:...4_:[.DG]G-----C[.DC]:..21_:B<....
5 20 0 # 5 | ....>A:...5_:[.DA]A-----T[.DT]:..20_:B<....
6 19 0 # 6 | ....>A:...6_:[.DA]A-----T[.DT]:..19_:B<....
7 18 0 # 7 | ....>A:...7_:[.DT]T-----A[.DA]:..18_:B<....
8 17 0 # 8 | ....>A:...8_:[.DT]T-----A[.DA]:..17_:B<....
9 16 0 # 9 | ....>A:...9_:[.DC]C-----G[.DG]:..16_:B<....
10 15 0 # 10 | ....>A:..10_:[.DG]G-----C[.DC]:..15_:B<....
11 14 0 # 11 | ....>A:..11_:[.DC]C-----G[.DG]:..14_:B<....
12 13 0 # 12 | ....>A:..12_:[.DG]G-----C[.DC]:..13_:B<....
------------------------------------------------------------------
analyze 355d.bps
# generate output file '355d.out', with base-pair step parameters:
****************************************************************************
step Shift Slide Rise Tilt Roll Twist
1 CG/CG 0.09 0.04 3.20 -3.22 8.52 32.73
2 GC/GC 0.50 0.67 3.69 2.85 -9.06 43.88
3 CG/CG -0.14 0.59 3.00 0.97 11.30 25.11
4 GA/TC -0.45 -0.14 3.39 -1.59 1.37 37.50
5 AA/TT 0.17 -0.33 3.30 -0.33 0.46 37.52
6 AT/AT -0.01 -0.60 3.22 -0.31 -2.67 32.40
7 TT/AA -0.08 -0.40 3.22 1.68 -0.97 33.74
8 TC/GA -0.27 -0.23 3.47 0.68 -1.69 42.14
9 CG/CG 0.70 0.78 3.07 -3.66 4.18 26.58
10 GC/GC -1.31 0.36 3.37 -2.85 -9.37 41.60
11 CG/CG -0.31 0.21 3.17 -0.68 6.69 33.31
****************************************************************************
Reversing the order of chains A and B in ‘355d.pdb’ as ‘355d-reversed.pdb’ and repeating the above procedure, we have the following results:
find_pair 355d-reversed.pdb 355d-reversed.bps
# contents of file '355d-reversed.bps':
------------------------------------------------------------------
355d-reversed.pdb
355d-reversed.out
2 # duplex
12 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
1 24 0 # 1 | ....>B:..13_:[.DC]C-----G[.DG]:..12_:A<....
2 23 0 # 2 | ....>B:..14_:[.DG]G-----C[.DC]:..11_:A<....
3 22 0 # 3 | ....>B:..15_:[.DC]C-----G[.DG]:..10_:A<....
4 21 0 # 4 | ....>B:..16_:[.DG]G-----C[.DC]:...9_:A<....
5 20 0 # 5 | ....>B:..17_:[.DA]A-----T[.DT]:...8_:A<....
6 19 0 # 6 | ....>B:..18_:[.DA]A-----T[.DT]:...7_:A<....
7 18 0 # 7 | ....>B:..19_:[.DT]T-----A[.DA]:...6_:A<....
8 17 0 # 8 | ....>B:..20_:[.DT]T-----A[.DA]:...5_:A<....
9 16 0 # 9 | ....>B:..21_:[.DC]C-----G[.DG]:...4_:A<....
10 15 0 # 10 | ....>B:..22_:[.DG]G-----C[.DC]:...3_:A<....
11 14 0 # 11 | ....>B:..23_:[.DC]C-----G[.DG]:...2_:A<....
12 13 0 # 12 | ....>B:..24_:[.DG]G-----C[.DC]:...1_:A<....
------------------------------------------------------------------
analyze 355d-reversed.bps
# generate output file '355d-reversed.out', with base-pair step parameters:
****************************************************************************
step Shift Slide Rise Tilt Roll Twist
1 CG/CG 0.31 0.21 3.17 0.68 6.69 33.31
2 GC/GC 1.31 0.36 3.37 2.85 -9.37 41.60
3 CG/CG -0.70 0.78 3.07 3.66 4.18 26.58
4 GA/TC 0.27 -0.23 3.47 -0.68 -1.69 42.14
5 AA/TT 0.08 -0.40 3.22 -1.68 -0.97 33.74
6 AT/AT 0.01 -0.60 3.22 0.31 -2.67 32.40
7 TT/AA -0.17 -0.33 3.30 0.33 0.46 37.52
8 TC/GA 0.45 -0.14 3.39 1.59 1.37 37.50
9 CG/CG 0.14 0.59 3.00 -0.97 11.30 25.11
10 GC/GC -0.50 0.67 3.69 -2.85 -9.06 43.88
11 CG/CG -0.09 0.04 3.20 3.22 8.52 32.73
****************************************************************************
Comparing the base-pair step parameters between ‘355d.out’ and ’355d-reversed.out’, one would notice that while slide/rise/roll/twist simply switch orders, shift/tilt (the x-axis parameters) also flip their signs. On the other hand, the nucleotide serial numbers specifying base pairs (the left two columns) are identical in ‘355d.bps’ and ’355d-reversed.bps’.
Apart from explicitly swapping the two strands in PDB data file, one can simply switch around the nucleotide serial numbers generated with find_pair in order to analyze a DNA duplex based on its complementary sequence instead of the primary one. For example, starting from the same PDB file ‘355d.pdb’, we change ‘355d.bps’ to ’355d-cs.bps’ as below,
------------------------------------------------------------------
355d.pdb
355d-cs.out
2 # duplex
12 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
13 12
14 11
15 10
16 9
17 8
18 7
19 6
20 5
21 4
22 3
23 2
24 1
------------------------------------------------------------------
Run analyze 355d-cs.bps, one would get exactly the same parameters in output file ’355d-cs.out’ as in ’355d-reversed.out’.
